I am not an expert, but I found one post here at RG platform, which may be helpful for you: https://www.researchgate.net/post/How_can_I_analyze_a_full_genome

Please Go To This Link:

Article Viral Genomics and Bioinformatics

Thanks @Abdelkader Mohamed Elsayed

There are tools developed by communities which are freely available and best for genomic analysis. One of them which I recommend is GaTk. https://gatk.broadinstitute.org/hc/en-us

You can easily find some tutorials for the same on YouTube.

@Anuj Singh.... Thanks

Ya I tried Gatk but most of the tutorial are for mammalian genome. And i am trying for bacterial genomes. Is it suitable for bacterial genomes too?

Yes indeed, most of the tutorials are based on mammalian genome but it is also suitable for bacterial genomics. You must refer the documentation and forum for the same.

I recommend reading this article:

https://www.frontiersin.org/articles/10.3389/fgene.2017.00072/full

I recommend BioCyc Database Collection

https://biocyc.org

Please see this Link:

https://www.broadinstitute.org/infectious-disease-and-microbiome/bacterial-genomics

Dear Dr. Sonti Roy ,

this link mybe important for you:

https://holtlab.net/2015/02/25/tools-for-bacterial-comparative-genomics/

Hi Sonti Roy . There are several tools available to analyse bacterial genomes. You pick the tools based on what questions you are trying to answer and what datasets you have at hand. If can tell what exactly you want to do you can get specific answers. But I will give some activities I perform with by genomes and I think you can adapt. I am assuming you have the raw illumina or nanopore rreads.

1. Trim data

2. Perform Genome assembly to generate contigs ( I have a video on that here : https://youtu.be/h8AuVoZl2Zo )

3. Reorder your your contigs.

4. Perform Genome annotation ( I made a video here : https://youtu.be/MqDhhuIXjgg )

5. Perform genome comparison using BRIG software ( here is a video to help you : https://youtu.be/pobQgE4z-5Q )

6. Perform Pangenome Analysis

There are more you can do . I recommend you read the document here : https://holtlab.net/tag/comparative-genomics/

Thanks Vincent Appiah